APPENDIX D - PDB Fat File Format 1.1
The PDB Fat (PDBF) file format is a custom version of the standard PDB that was created to include extra information, normally not allowed, keeping the compatibility with the Brookhaven National Library specifications. A sequence of REMARK records (one for each atom) was added at the beginning of file. The REMARK type is the user defined REMARK 77 (see PDB specifications) followed by the EXTRA keyword. This rule was introduced recognize the custom records from standard REMARKs. In each REMARK record are included the following information: atom number, element, atom type (according to force field) and the atomic partial charge:
1 2 3 4 1234567890123456789012345678901234567890123 REMARK 77 EXTRA NNNNN EE FFFFFFFF CC.CCCC NNNNN <- Atom number (C: %5d, Fortran: i5) EE <- Element (C: %-2.2s, Fortran: a2) FFFFFFFF <- Atom type (C: %-8.8s, Fortran: a8) CC.CCCC <- Atom charge (C: %7.4f, Fortran: f7.4)
Warning:
Starting from 1.1 specifications, introduced in VEGA 1.5.0, the atom type
format is changed in order to support atom types with more than four
characters (the limit is now eight characters). The old 1.0
specifications are supported by VEGA in read mode for backward compatibility.
Example:
Benzene ring with CVFF atom types and Gasteiger atom charges.
REMARK 4 REMARK 4 File converted by VEGA V1.1 REMARK 4 REMARK 77 EXTRA 1 C cp -0.0618 REMARK 77 EXTRA 2 C cp -0.0618 REMARK 77 EXTRA 3 C cp -0.0618 REMARK 77 EXTRA 4 C cp -0.0618 REMARK 77 EXTRA 5 C cp -0.0618 REMARK 77 EXTRA 6 C cp -0.0618 REMARK 77 EXTRA 7 H h 0.0618 REMARK 77 EXTRA 8 H h 0.0618 REMARK 77 EXTRA 9 H h 0.0618 REMARK 77 EXTRA 10 H h 0.0618 REMARK 77 EXTRA 11 H h 0.0618 REMARK 77 EXTRA 12 H h 0.0618 ATOM 1 C1 BEN 1 0.695 1.203 0.000 1.00 0.00 ATOM 2 C2 BEN 1 -0.695 1.203 -0.002 1.00 0.00 ATOM 3 C3 BEN 1 -1.389 0.000 -0.006 1.00 0.00 ATOM 4 C4 BEN 1 -0.695 -1.203 -0.007 1.00 0.00 ATOM 5 C5 BEN 1 0.695 -1.203 -0.006 1.00 0.00 ATOM 6 C6 BEN 1 1.389 0.000 -0.002 1.00 0.00 ATOM 7 H7 BEN 1 1.235 2.139 0.003 1.00 0.00 ATOM 8 H8 BEN 1 -1.235 2.139 -0.001 1.00 0.00 ATOM 9 H9 BEN 1 -2.470 0.000 -0.007 1.00 0.00 ATOM 10 H10 BEN 1 -1.235 -2.139 -0.010 1.00 0.00 ATOM 11 H11 BEN 1 1.235 -2.139 -0.007 1.00 0.00 ATOM 12 H12 BEN 1 2.470 0.000 -0.001 1.00 0.00 TER 13 BEN 1 CONECT 1 2 6 7 CONECT 2 1 3 8 CONECT 3 2 4 9 CONECT 4 3 5 10 CONECT 5 4 6 11 CONECT 6 1 5 12 CONECT 7 1 CONECT 8 2 CONECT 9 3 CONECT 10 4 CONECT 11 5 CONECT 12 6 MASTER 15 0 0 0 0 0 0 0 12 1 12 0 END